Analysis of the algorithm: From kernels to prioritized genes.

Kernelization section

The algorithm transformed the semantic similarity matrix to make it compatible with a kernel. Once this was done for each network and kernel type, it was integrated by kernel type. Below there is a general analysis of the properties of each matrix in the different phases of the process.

Annotations properties

Table 1. Annotation files descriptors

Net Min Max Average Standard_Deviation
DepMap_effect 972 17354 2043.6562906724512 3829.1218209282715
biological_process 1 1053 8.255678448065316 20.730757162592834
cellular_component 1 5172 7.219656420451649 82.56741928666138
disease 1 81 1.7829472267615112 2.3512948371338793
gene_PS 1 108 2.1519058295964126 5.045578888786698
gene_TF 1 5778 3.0320060963993143 74.46796191948712
gene_hgncGroup 1 2294 2.261042369703787 23.27548667222241
hippie_ppi 1 2985 84.68724915097252 150.1286010250888
molecular_function 1 6791 4.87167748867193 54.08093332133869
pathway 1 479 6.75436035343834 16.179001796162975
phenotype 1 1307 23.941396322320227 48.71098651648341
string_ppi 1 7338 610.0699285559645 500.6662722348227

Matrix properties

Table 2. Similarity matrixes

Net Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
DepMap_effect_bicor_sim 17354x17354 301161316 106761316 0.35449876968926514
biological_process_sim 16979x16979 288286441 256362631 0.8892635744877089
cellular_component_sim 17963x17963 322669369 320867108 0.9944145271502359
disease_sim 4162x4162 17322244 17228280 0.9945755295907389
gene_PS_sim 362x362 131044 1666 0.012713287140197186
gene_TF_sim 1044x1044 1089936 172858 0.15859463307937346
gene_hgncGroup_sim 25136x25136 631818496 14457654 0.022882606462980154
hippie_ppi_sim 19434x19434 377680356 1630698 0.0043176669744507444
molecular_function_sim 17333x17333 300432889 296572456 0.9871504314562578
pathway_sim 3429x3429 11758041 159182 0.013538139559132342
phenotype_sim 5077x5077 25775929 25699341 0.9970287006920294
string_ppi_sim 18476x18476 341362576 11271627 0.03301951588272523

Table 3. Filtered similarity matrixes

Net Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
string_ppi_sim 16111x16111 259564321 480917 0.001852785460448549

Table 4. Uncombined kernel matrixes

Net Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
DepMap_effect_bicor ct 17354x17354 301161316 301161316 1.0
DepMap_effect_bicor el 17354x17354 301161316 301161316 1.0
DepMap_effect_bicor ka 17354x17354 301161316 106778670 0.35455639329189276
DepMap_effect_bicor rf 17354x17354 301161316 301161316 1.0
biological_process ct 16979x16979 288286441 288286441 1.0
biological_process el 16979x16979 288286441 288286441 1.0
biological_process ka 16979x16979 288286441 256366715 0.8892777409534846
biological_process rf 16979x16979 288286441 288286441 1.0
cellular_component ct 17963x17963 322669369 322669369 1.0
cellular_component el 17963x17963 322669369 322669369 1.0
cellular_component ka 17963x17963 322669369 320870945 0.9944264185795708
cellular_component rf 17963x17963 322669369 322669369 1.0
disease ct 4162x4162 17322244 17322244 1.0
disease el 4162x4162 17322244 17322244 1.0
disease ka 4162x4162 17322244 17230892 0.9947263183684516
disease rf 4162x4162 17322244 17322244 1.0
gene_PS ct 362x362 131044 111955 0.8543313696163121
gene_PS el 362x362 131044 7680 0.05860626964988859
gene_PS ka 362x362 131044 2028 0.015475718079423705
gene_PS node2vec 362x362 131044 131044 1.0
gene_PS rf 362x362 131044 7680 0.05860626964988859
gene_TF ct 1044x1044 1089936 1089918 0.9999834852688598
gene_TF el 1044x1044 1089936 1062998 0.9752847873636618
gene_TF ka 1044x1044 1089936 173902 0.15955248748550374
gene_TF node2vec 1044x1044 1089936 1089936 1.0
gene_TF rf 1044x1044 1089936 1062998 0.9752847873636618
gene_hgncGroup ct 25136x25136 631818496 631304330 0.9991862124909999
gene_hgncGroup el 25136x25136 631818496 326932198 0.5174463870079549
gene_hgncGroup ka 25136x25136 631818496 14482790 0.022922390040319426
gene_hgncGroup rf 25136x25136 631818496 326932198 0.5174463870079549
hippie_ppi ct 19434x19434 377680356 377680356 1.0
hippie_ppi el 19434x19434 377680356 377214096 0.9987654639893424
hippie_ppi ka 19434x19434 377680356 1645226 0.004356133364796976
hippie_ppi node2vec 19434x19434 377680356 377680356 1.0
hippie_ppi rf 19434x19434 377680356 377214096 0.9987654639893424
molecular_function ct 17333x17333 300432889 300432889 1.0
molecular_function el 17333x17333 300432889 300432889 1.0
molecular_function ka 17333x17333 300432889 296576663 0.9871644345835918
molecular_function rf 17333x17333 300432889 300432889 1.0
pathway ct 3429x3429 11758041 11744213 0.9988239537521599
pathway el 3429x3429 11758041 8641125 0.7349119636510878
pathway ka 3429x3429 11758041 162611 0.013829769772022398
pathway node2vec 3429x3429 11758041 11758041 1.0
pathway rf 3429x3429 11758041 8641125 0.7349119636510878
phenotype ct 5077x5077 25775929 25775929 1.0
phenotype el 5077x5077 25775929 25775929 1.0
phenotype ka 5077x5077 25775929 25700323 0.997066798251966
phenotype rf 5077x5077 25775929 25775929 1.0
string_ppi ct 16111x16111 259564321 259564321 1.0
string_ppi el 16111x16111 259564321 252333871 0.9721438987756719
string_ppi ka 16111x16111 259564321 497009 0.0019147816544478006
string_ppi node2vec 16111x16111 259564321 259564321 1.0
string_ppi rf 16111x16111 259564321 252333871 0.9721438987756719

Table 5. Integrated kernel matrixes

Integration Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
integration_mean_by_presence ct 30584x30584 935381056 824239788 0.8811807580588846
integration_mean_by_presence el 30584x30584 935381056 612690734 0.655017257480143
integration_mean_by_presence ka 30584x30584 935381056 367554852 0.3929466495417243
integration_mean_by_presence node2vec 19949x19949 397962601 393142685 0.9878885202079579
integration_mean_by_presence rf 30584x30584 935381056 612690734 0.655017257480143
mean ct 30584x30584 935381056 824239788 0.8811807580588846
mean el 30584x30584 935381056 612690734 0.655017257480143
mean ka 30584x30584 935381056 367554852 0.3929466495417243
mean node2vec 19949x19949 397962601 393142685 0.9878885202079579
mean rf 30584x30584 935381056 612690734 0.655017257480143

Weight values